Protein
Protein Proteins comprise one of the major groups of biological macromolecules and have a variety of roles within the body (most notably as enzymes or providing structural support). They are also known as polypeptides as they are composed of one or more chains of amino acids. There are 20 common amino acids glycine, alanine, proline, valine, isoleucine, leucine, methionine, serine, threonine, cysteine, asparagine, glutamine, glutamate, phenylalanine, tryptophan, tyrosine, lysine, arginine, and histidine. It should be noted that other amino acids exist and are incorporated into proteins. Each amino acid has unique chemical features that include being polar, nonpolar, aromatic, positive, negative, small, or large. The individual properties of the amino acid can give the protein or regions of the protein structural characteristics and this is important as protein structure is related to protein function. Protein Structure Protein structure is generally characterized at four different levels: primary, secondary, tertiary, and quarternary structure. *Primary structure simply refers to the order of amino acids in the polypeptide chain. On average polypeptide chains are between 100 and 1000 amino acids long.(1) Given a polypeptides length(n) and knowing that only common amino acids will be found, there are 20^n possible sequences. (1) *Secondary structure refers to folding patterns within a region of the polypeptide chain. These can be alpha helices, beta sheets, or different turns. :::: Alpha helices have 3.6 amino acids per turn and attach to the amino acids above or below through hydrogen bonds. The hydrogen bonds are between the C=O group and N-H groups. (see figure to the left) :::: Beta Sh eets are rows of amino acids that also bind together using hydrogen bonds between a C=O group and N-H group. The rows can be described as being parallel or anti-parallel. Parallel strands run in the N to C direction (amino acids all have an amino group (NH2) on one side and a carboxylic acid group on the other (COOH). When amino acids form a chain these two groups will bond). Anti-parallel strands will have one group going from N to C and the other from C to N. *Tertiary structure refers to the overall structure of the polypeptide chain. Therefore this includes regions with alpha helices, beta sheets, and regions of unclassified structure. (See figure to the left). *Quartenary structure refers to the overall structure of more than one polypeptide chain. (These are NOT two separate proteins, just two subunits of a protein.) How are proteins made? Transcription Each protein sequence is encoded within an organism's DNA. While DNA contains only four bases (adenine, guanine, cytosine, and thymine), the arrangement of the bases are what encodes different proteins. In transcription the region of DNA that contains a protein sequence converted into the complement sequence in RNA via RNA polymerase. This RNA is also known as mRNA. The mRNA may undergo modifications known as mRNA processing or post-transcriptional modification in some organisms. Translation In translation, the mRNA associates with a ribosome and multiple tRNAs. Each tRNA contains a 3 code sequence. Starting with the 5' end of the mRNA, a tRNA will match its three bases with three bases in mRNA. This will continue moving from the 5' to 3' end. Each tRNA is also connected to an amino acid and another tRNA is able to bind the amino acids link together